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cuffdiff: use merged.gtf from cuffmerge or combined.gtf from cuffcompare? turnersd Bioinformatics 21 10-02-2014 03:41 AM
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^@ in .combined.gtf from cuffcompare v0.8.4 glacierbird Bioinformatics 2 01-14-2011 12:42 PM
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Old 05-30-2011, 12:36 PM   #1
julio514
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Default cuffcompare only generates .gtf.tmap and .gtf.refmap?

Hi all,

I've been able to run a tophat/cufflinks with no prob. However, when I run cuffcompare, it only gives me the .gtf.tmap and .gtf.refmap files with no <outprefix>, <outprefix>combined.gtf, and <outprefix>.tracking files.

My cuffcompare command looks something like this.

cuffcompare -V -r blabla.gff -s blabla.fa tanscripts_1.gtf transcripts_2. gtf and so on...

Anyone ever encountered this issue?
Cheers,
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Old 07-14-2011, 05:56 AM   #2
hibachings2013
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i just got the same situation. have you resolved this problem??
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Old 07-14-2011, 10:27 PM   #3
julio514
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Unfortunately no. I haven't try to solve this issue since a couple of months though. I'm wondering if it has to do with the fact that I am comparing samples with no replicates... Are you trying Cufcompare with replicates?
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Old 07-15-2011, 04:03 AM   #4
hibachings2013
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yes, data i use have replicates.
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Old 07-15-2011, 04:18 AM   #5
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and each of the lanes correspond to a pooled sample of 5-6 replicates.
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